J Gregory Caporaso

Summary

Publications

  1. pmc Moving pictures of the human microbiome
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, CO 80309, USA
    Genome Biol 12:R50. 2011
  2. pmc Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
    Nicholas A Bokulich
    Department of Viticulture and Enology, University of California, Davis, Davis, California, USA
    Nat Methods 10:57-9. 2013
  3. pmc The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
    Daniel McDonald
    Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA
    Gigascience 1:7. 2012
  4. pmc MutationFinder: a high-performance system for extracting point mutation mentions from text
    J Gregory Caporaso
    Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora, CO, USA
    Bioinformatics 23:1862-5. 2007
  5. ncbi request reprint Rapid pattern development for concept recognition systems: application to point mutations
    J Gregory Caporaso
    Department of Biochemistry and Molecular Genetics, Center for Computational Pharmacology, University of Colorado Health Sciences Center, Aurora, CO, USA
    J Bioinform Comput Biol 5:1233-59. 2007
  6. pmc Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
    BMC Evol Biol 8:327. 2008
  7. pmc Host-associated and free-living phage communities differ profoundly in phylogenetic composition
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado, United States of America
    PLoS ONE 6:e16900. 2011
  8. doi request reprint Diversity, distribution and sources of bacteria in residential kitchens
    Gilberto E Flores
    Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA
    Environ Microbiol 15:588-96. 2013
  9. doi request reprint Using QIIME to analyze 16S rRNA gene sequences from microbial communities
    Justin Kuczynski
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
    Curr Protoc Microbiol . 2012
  10. pmc PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers
    William A Walters
    Department of Molecular, Cellular, and Developmental Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, CO 80309, USA
    Bioinformatics 27:1159-61. 2011

Collaborators

Detail Information

Publications29

  1. pmc Moving pictures of the human microbiome
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado, 215 UCB, Boulder, CO 80309, USA
    Genome Biol 12:R50. 2011
    ..Here, we present the largest human microbiota time series analysis to date, covering two individuals at four body sites over 396 timepoints...
  2. pmc Quality-filtering vastly improves diversity estimates from Illumina amplicon sequencing
    Nicholas A Bokulich
    Department of Viticulture and Enology, University of California, Davis, Davis, California, USA
    Nat Methods 10:57-9. 2013
    ..We present guidelines for user-defined quality-filtering strategies, enabling efficient extraction of high-quality data and facilitating interpretation of Illumina sequencing results...
  3. pmc The Biological Observation Matrix (BIOM) format or: how I learned to stop worrying and love the ome-ome
    Daniel McDonald
    Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA
    Gigascience 1:7. 2012
    ....
  4. pmc MutationFinder: a high-performance system for extracting point mutation mentions from text
    J Gregory Caporaso
    Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Aurora, CO, USA
    Bioinformatics 23:1862-5. 2007
    ..We present an open-source, rule-based system, MutationFinder, for extracting point mutation mentions from text. On blind test data, it achieves nearly perfect precision and a markedly improved recall over a baseline...
  5. ncbi request reprint Rapid pattern development for concept recognition systems: application to point mutations
    J Gregory Caporaso
    Department of Biochemistry and Molecular Genetics, Center for Computational Pharmacology, University of Colorado Health Sciences Center, Aurora, CO, USA
    J Bioinform Comput Biol 5:1233-59. 2007
    ..Both MutationFinder and the complete corpus are publicly available at (http://mutationfinder.sourceforge.net/)...
  6. pmc Detecting coevolution without phylogenetic trees? Tree-ignorant metrics of coevolution perform as well as tree-aware metrics
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
    BMC Evol Biol 8:327. 2008
    ..We further considered the influence of sequence recoding using reduced-state amino acid alphabets, a common tactic employed in coevolutionary analyses to improve both statistical and computational performance...
  7. pmc Host-associated and free-living phage communities differ profoundly in phylogenetic composition
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, Colorado, United States of America
    PLoS ONE 6:e16900. 2011
    ....
  8. doi request reprint Diversity, distribution and sources of bacteria in residential kitchens
    Gilberto E Flores
    Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA
    Environ Microbiol 15:588-96. 2013
    ..These results also illustrate the ease with which human- and food-associated bacteria can be transferred in residential settings to kitchen surfaces...
  9. doi request reprint Using QIIME to analyze 16S rRNA gene sequences from microbial communities
    Justin Kuczynski
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
    Curr Protoc Microbiol . 2012
    ..The following protocols describe how to install QIIME on a single computer and use it to analyze microbial 16S sequence data from nine distinct microbial communities...
  10. pmc PrimerProspector: de novo design and taxonomic analysis of barcoded polymerase chain reaction primers
    William A Walters
    Department of Molecular, Cellular, and Developmental Biology, Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Boulder, CO 80309, USA
    Bioinformatics 27:1159-61. 2011
    ..PCR amplification of DNA is a key preliminary step in many applications of high-throughput sequencing technologies, yet design of novel barcoded primers and taxonomic analysis of novel or existing primers remains a challenging task...
  11. pmc Using QIIME to analyze 16S rRNA gene sequences from microbial communities
    Justin Kuczynski
    Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, Colorado, USA
    Curr Protoc Bioinformatics . 2011
    ..The following protocols describe how to install QIIME on a single computer and use it to analyze microbial 16S sequence data from nine distinct microbial communities...
  12. pmc Examining the global distribution of dominant archaeal populations in soil
    Scott T Bates
    Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA
    ISME J 5:908-17. 2011
    ..This trend was coupled with a concurrent increase in known N-oxidizing bacteria, suggesting competitive interactions between these groups...
  13. ncbi request reprint Advancing our understanding of the human microbiome using QIIME
    José A Navas-Molina
    Department of Computer Science, University of Colorado, Boulder, Colorado, USA
    Methods Enzymol 531:371-444. 2013
    ..We present examples of some of the types of analyses that are enabled by QIIME and discuss how other tools, such as phyloseq and R, can be applied to expand upon these analyses. ..
  14. pmc Cross-biome metagenomic analyses of soil microbial communities and their functional attributes
    Noah Fierer
    Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 109:21390-5. 2012
    ....
  15. pmc TopiaryExplorer: visualizing large phylogenetic trees with environmental metadata
    Meg Pirrung
    Department of Pharmacology, University of Colorado Denver, Aurora, CO 80045, USA
    Bioinformatics 27:3067-9. 2011
    ....
  16. pmc The interpersonal and intrapersonal diversity of human-associated microbiota in key body sites
    Luke K Ursell
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
    J Allergy Clin Immunol 129:1204-8. 2012
    ....
  17. pmc Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, CO 80309, USA
    Proc Natl Acad Sci U S A 108:4516-22. 2011
    ..The results thus open up the possibility of conducting large-scale studies analyzing thousands of samples simultaneously to survey microbial communities at an unprecedented spatial and temporal resolution...
  18. pmc PyCogent: a toolkit for making sense from sequence
    Rob Knight
    Department of Chemistry and Biochemistry, University of Colorado, Boulder, Colorado, USA
    Genome Biol 8:R171. 2007
    ..The toolkit takes advantage of parallel architectures and runs on a range of hardware and operating systems, and is available under the general public license from http://sourceforge.net/projects/pycogent...
  19. pmc Phylogenetic stratigraphy in the Guerrero Negro hypersaline microbial mat
    J Kirk Harris
    Department of Pediatrics, School of Medicine, University of Colorado Denver, Aurora, CO, USA
    ISME J 7:50-60. 2013
    ....
  20. pmc Ultra-high-throughput microbial community analysis on the Illumina HiSeq and MiSeq platforms
    J Gregory Caporaso
    Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA
    ISME J 6:1621-4. 2012
    ....
  21. ncbi request reprint Error minimization and coding triplet/binding site associations are independent features of the canonical genetic code
    J Gregory Caporaso
    Department of Biochemistry and Molecular Genetics, University of Colorado Health Sciences Center, Mail Stop 8303, P O Box 6511, Aurora, CO 80045, USA
    J Mol Evol 61:597-607. 2005
    ..We explicitly show that prior fixation of a stereochemical core is consistent with an effective later minimization of error...
  22. pmc The Western English Channel contains a persistent microbial seed bank
    J Gregory Caporaso
    Department of Computer Science, Northern Arizona University, Flagstaff, AZ, USA
    ISME J 6:1089-93. 2012
    ..Thus observed changes in community composition are actually variations in the relative abundance of taxa, not, as was previously believed, demonstrating extinction and recolonization of taxa in the ecosystem through time...
  23. pmc Cohabiting family members share microbiota with one another and with their dogs
    Se Jin Song
    Department of Ecology and Evolutionary Biology, University of Colorado, Boulder, Boulder, United States
    elife 2:e00458. 2013
    ..DOI:http://dx.doi.org/10.7554/eLife.00458.001...
  24. pmc Concept recognition for extracting protein interaction relations from biomedical text
    William A Baumgartner
    Center for Computational Pharmacology, University of Colorado School of Medicine, Aurora, Colorado 80045, USA
    Genome Biol 9:S9. 2008
    ..The BioCreative II tasks discussed in this special issue have provided a unique opportunity to demonstrate the effectiveness of concept recognition in the field of biomedical language processing...
  25. pmc PyNAST: a flexible tool for aligning sequences to a template alignment
    J Gregory Caporaso
    Department of Chemistry and Biochemistry, University of Colorado at Boulder, Boulder, CO, USA
    Bioinformatics 26:266-7. 2010
    ..Python Nearest Alignment Space Termination (PyNAST) is a complete reimplementation of NAST, which includes three convenient interfaces: a Mac OS X GUI, a command-line interface and a simple application programming interface (API)...
  26. pmc Bacterial diversity in two Neonatal Intensive Care Units (NICUs)
    Krissi M Hewitt
    Department of Biology, San Diego State University, San Diego, California, United States of America
    PLoS ONE 8:e54703. 2013
    ..Our findings provide evidence that NICU IHEs harbor a high diversity of human-associated bacteria and demonstrate the potential utility of molecular methods for identifying and tracking bacterial diversity in NICUs...
  27. pmc Bacterial communities associated with the lichen symbiosis
    Scott T Bates
    Cooperative Institute for Research in Environmental Sciences, University of Colorado at Boulder, Rm 318, CIRES Bldg, Boulder, CO 80309, USA
    Appl Environ Microbiol 77:1309-14. 2011
    ..Our findings confirm the presence of highly structured bacterial communities within lichens and provide additional evidence that these bacteria may serve distinct functional roles within lichen symbioses...
  28. ncbi request reprint Origins of the genetic code: the escaped triplet theory
    Michael Yarus
    Department of Molecular Cellular and Developmental Biology, University of Colorado, Boulder, Colorado 80309 0347, USA
    Annu Rev Biochem 74:179-98. 2005
    ..These data also strengthen the argument for invention of the genetic code in an RNA world and for the RNA world itself...